Option value constant to vague handling of aromaticity; In the query all
single ring bonds are replaced by "single or aromatic" and all double
ring bonds are replaced by "double or aromatic" prior to search.

SIMILARITY

FULL

static final int FULL

Full structure search. (Prior to version 5.2 called EXACT.)
Query and target must have the same heavy atom (non-H) network for
matching. All other properties are otherwise evaluated the same way as
substructure search. Please note that this search type is not suitable
for equality check. For that, please use DUPLICATE search type.
(Value=4)

DUPLICATE

static final int DUPLICATE

Duplicate search (formerly called perfect).
Used for deciding absolute equality of molecular
features (eg duplicate check before database insert). Equality is always
subject to standardization in the database. Query features are
not evaluated. (Value=5)
For this search mode there is no search per minute license limitation
in JChemBase, these searches are not counted.

STEREO_IGNORE

STEREO_EXACT

static final int STEREO_EXACT

Equality is needed in stereochemistry. ("All stereo info is
exactly the same.") It mainly has an effect when the query has no stereo
information: it only matches non-stereo target. Similarly, a query with
a wiggly tetrahedral center will only match wiggly tetrahedral center,
and not specific R and S configurations. If STEREO_SPECIFIC is set, non-stereo query
matches both nonstereo and stereo target.

STEREO_DIASTEREOMER

static final int STEREO_DIASTEREOMER

The diastereomers targets
of a given query structure are also matched. This means that it is only required
that if a query atom has stereo information, the target atom should have as well
but the two configurations are treated the same.

DISSIMILARITY_PROPERTY_NAME

HCOUNT_MATCHING_AUTO

static final int HCOUNT_MATCHING_AUTO

Default option for H count matching (setHCountMatching).
The search tries to find out from the source of the query structure
which H count matching option to use. (HCOUNT_MATCHING_EQUAL for
smiles and smarts, and HCOUNT_MATCHING_GREATER_OR_EQUAL for mdl
molfiles.)

HCOUNT_MATCHING_EQUAL

static final int HCOUNT_MATCHING_EQUAL

Option for H count matching. Means that a query atom with H count
should only match a target atom with hydrogens (implicit or explicit)
equal to the H count. This is the Daylight(smiles, smarts) behaviour.

HCOUNT_MATCHING_GREATER_OR_EQUAL

static final int HCOUNT_MATCHING_GREATER_OR_EQUAL

Option for H count matching. Means that a query atom with H count
should only match a target atom with hydrogens (implicit or explicit)
equal to or greater than the H count. One exception is H count = 0, which
means no Hydrogens extra to those explicitly drawn.
This is the MDL(sd, molfile) behaviour.

VAGUE_BOND_OFF

VAGUE_BOND_LEVEL1

static final int VAGUE_BOND_LEVEL1

Until 5.3 it was an option value constant to handle some ambiguous
aromaticity, 5-membered Kekule representation queries. From 5.3 extends
to 1-atom ligands of aromatic rings and 1 long connections between
aromatic rings also (default from 5.3 to 15.9.14).

VAGUE_BOND_LEVEL_HALF

static final int VAGUE_BOND_LEVEL_HALF

Option value constant to handle some ambiguous aromaticity, 5-membered
Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1
S1C=CC=C1. This is the default value before 5.3 and after 15.9.14.

VAGUE_BOND_DEFAULT

VAGUE_BOND_LEVEL2

static final int VAGUE_BOND_LEVEL2

Option value constant to vague handling of aromaticity; In the query all
single ring bonds are replaced by "single or aromatic" and all double
ring bonds are replaced by "double or aromatic" prior to search.
(Caution: Not very efficient during fingerprint screening!)

VAGUE_BOND_LEVEL3

static final int VAGUE_BOND_LEVEL3

Option value constant to vague handling of aromaticity; In the query all
single bonds are replaced by "single or aromatic" and all double bonds
are replaced by "double or aromatic" prior to search. (Caution: very
inefficient during fingerprint screening!)

STEREO_MODEL_LOCAL

static final int STEREO_MODEL_LOCAL

Option value constant to use local stereo information only (local parity,
local double bond stereo configuration, etc). This is useful for
substructure search. When a symmetric atom/bond in the query is
specified, this method only matches target atoms/bonds with specified
stereochemistry. (For example, query C[C@](C)(C)C does not match
CC(C)(C)C.)

STEREO_MODEL_COMPREHENSIVE

static final int STEREO_MODEL_COMPREHENSIVE

Option value constant to use comprehensive stereo model, which combines
the advantages of local and global stereo models. This setting
is suitable for all search types. In principle, it is similar to the
local stereo model, except when the target is symmetrical. In the
symmetrical target case the matching is accepted, regardless of stereo
information. For example, substructure query C[C@](C)(C)C matches both
CC(C)(C)C , C[C@@](C)(C)C and CCC[C@@](C)(CC)C(C)C.

STEREO_MODEL_GLOBAL

static final int STEREO_MODEL_GLOBAL

Option value constant to use global stereo information (global
parity, global double bond stereo configuration, etc). This value is
suitable for duplicate, full and full fragment searches, as in these
cases the full stereospecific environment is always available for both
the query and target structures. (Therefore a symmetrical atom/bond with
stereo configuration may match to an unspecified strereo atom/bond.
For example, C[C@](C)(C)C matches CC(C)(C)C.)

IMPLICIT_H_MATCHING_DEFAULT

static final int IMPLICIT_H_MATCHING_DEFAULT

Option value constant for default mode.
Its value is IMPLICIT_H_MATCHING_ENABLED in almost every cases.
There is only one exception: in case of duplicate search against
a query table in a database the default value is
IMPLICIT_H_MATCHING_DISABLED.

IMPLICIT_H_MATCHING_ENABLED

static final int IMPLICIT_H_MATCHING_ENABLED

Option value constant for indicate matching between implicit and
explicit hydrogens. In case of duplicate search the sum of implicit
and explicit hydrogens of the query atom and the sum on the matched
target atom must equal.

IMPLICIT_H_MATCHING_IGNORE

static final int IMPLICIT_H_MATCHING_IGNORE

Option value constant to indicate that hydrogens, either explicit
or implicit, are ignored during searching. Hydrogens having special
properties (radical, charge, isotope or more/less than one bond) are still
considered.
Option
CHARGE_MATCHING_IGNORE forces IMPLICIT_H_MATCHING_IGNORE in case of
duplicate search. In case of duplicate search against a query table in a
database IMPLICIT_H_MATCHING_IGNORE is switched to
IMPLICIT_H_MATCHING_DISABLED.
Hydrogens receive the excluded atom hit index HIT_EXCLUDEDQ
in this case.